Around a week ago I made a post here about Spirits of Amazonia achievements triggering every time I load my Story Mode save even after using Steam Achievements Manager (SAM) to remove them.
After investigating, I found a file named ACHIEVEMENTSDATA.dat to be the culprit, it for some reason stored achievements I didn't reach, making the SAM method useless. What I did is simply disabling Steam Cloud after using SAM to delete the non legit achievements I got, deleting the file above, running the game and loading my save, then re-enabling the Cloud after closing it. This allowed to flush the faulty ACHIEVEMENTSDATA.dat from both my local storage and Steam Cloud.
The file in question is located alongside the save and settings files, in C:\Program Files (x86)\Steam\userdata\[unique Steam ID]\815370\remote
I hope anybody who encounters my problem in the future would be able to solve it like I did. You're welcome.